17-44207502-G-C

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_ModerateBP7BS2

The NM_014233.4(UBTF):ā€‹c.2121C>Gā€‹(p.Gly707Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,874 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)
Exomes š‘“: 0.0000034 ( 0 hom. )

Consequence

UBTF
NM_014233.4 synonymous

Scores

1
3
12

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.744
Variant links:
Genes affected
UBTF (HGNC:12511): (upstream binding transcription factor) This gene encodes a member of the HMG-box DNA-binding protein family. The encoded protein plays a critical role in ribosomal RNA transcription as a key component of the pre-initiation complex, mediating the recruitment of RNA polymerase I to rDNA promoter regions. The encoded protein may also play important roles in chromatin remodeling and pre-rRNA processing, and its activity is regulated by both phosphorylation and acetylation. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. Pseudogenes of this gene are located on the short arm of chromosomes 3, 11 and X and the long arm of chromosome 11. [provided by RefSeq, Aug 2011]
ATXN7L3-AS1 (HGNC:55298): (ATXN7L3 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.11208868).
BP7
Synonymous conserved (PhyloP=-0.744 with no splicing effect.
BS2
High AC in GnomAdExome4 at 5 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
UBTFNM_014233.4 linkc.2121C>G p.Gly707Gly synonymous_variant Exon 20 of 21 ENST00000436088.6 NP_055048.1 P17480-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
UBTFENST00000436088.6 linkc.2121C>G p.Gly707Gly synonymous_variant Exon 20 of 21 2 NM_014233.4 ENSP00000390669.1 P17480-1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD3 exomes
AF:
0.00000398
AC:
1
AN:
251364
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
135852
show subpopulations
Gnomad AFR exome
AF:
0.0000615
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000342
AC:
5
AN:
1461874
Hom.:
0
Cov.:
33
AF XY:
0.00000275
AC XY:
2
AN XY:
727244
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000360
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
0.15
D
BayesDel_noAF
Pathogenic
0.16
CADD
Benign
1.1
DANN
Benign
0.30
DEOGEN2
Benign
0.0058
T
Eigen
Benign
-0.67
Eigen_PC
Benign
-0.71
FATHMM_MKL
Benign
0.16
N
LIST_S2
Benign
0.22
T
M_CAP
Uncertain
0.11
D
MetaRNN
Benign
0.11
T
MetaSVM
Uncertain
0.64
D
PROVEAN
Benign
0.46
N
REVEL
Benign
0.29
Sift
Benign
0.84
T
Sift4G
Benign
0.64
T
Vest4
0.18
MutPred
0.21
Gain of loop (P = 0.0195);
MVP
0.53
ClinPred
0.018
T
GERP RS
-0.77

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs148770098; hg19: chr17-42284870; API